Commenting on my own answer (bad form, yes) but it appears that it is possible using the -width method to get infinitely long lines. If $lineWidthValue == -1 the sequence will be output as a single line. There is a caveat however; if your pass '-1' to -width then write_seq does not print a newline at the end of the sequence as it normally would. You would need to manually print a newline to your output stream.
How To Write Sequences To Fasta Format With No Linebreaks (Wide Format) Using Bioperl
I'm trying to export aligned sequences to a fasta file one by one using Bio::SeqIO.
The result is that the sequences are broken by a new line every 60 columns.
How do I avoid that?
I'd like to have the sequences exported in a 'wide' format, i.e. no line breaks in the sequence.
My code is roughly:
use Bio::SeqIO;
my $seqin = Bio::SeqIO->new(-file => "<$fastaFile", '-format' => 'Fasta');
my $outname = fileparse($fastaFile, qr/\.[^\.]*$/) . "_sub.fasta";
my $seqout = Bio::SeqIO->new(-file => ">$outname", '-format' => 'Fasta');
while(my $seq = $seqin->next_seq){
# do something with $seq
$seqout->write_seq($seq);
}
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Biostar
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angel.roey •
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angel.roey •
2 answers
Yes, there is a simple parameter for controlling the width of the output, called surprisingly -width.
my $seqout = Bio::SeqIO->new(-file=>"$outFile", -format=>'Fasta', -width=>"$lineWidthValue")
The value of -width appears to be limited to 32,766 (i.e. essentially 2^15) so it isn't possible to write infinitely long lines with this method.
If $lineWidthValue is not defined, or == 0 the output will default to 60 characters per line.
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Alex Reynolds
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kmcarr00
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kmcarr00
I don't know bioperl, but I would circumvent the problem by opening $seqout as
open($seqout,'>',$outname);and outputting as
print $seqout ">",$seq->header,"\n",$seq->sequence,"\n";
Do replace $seq->header and $seq->sequence with the appropriate variables/methods.
(don't forget to close $seqout)
Yep, my way of circumventing it was exactly that -- open a file handle and print $seq->header and $seq->sequence to that file. But I thought there must be a more elegant way.
@Kenosis what would be the solution then? Is there a method for a wide fasta format in Bio::SeqIO?
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emphasized textIs there a method for a wide fasta format in Bio::SeqIO?
I haven't found one--yet--either googling or by examining the Bio::SeqIO and Bio::Seq modules. The OP's also posted the question at StackOverflow with no responses as of the time of this reply.
This is not true. Sometimes you want to pass a filehandle and not a filename, this is perfectly acceptable and there's a method for that, also :). For example, if you have the lexical filehandle $in, you'd pass the key/values of "-fh => \*$in" to the method new (instead of the familiar "-file => $filename").
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"...the sequences are broken by a new line every 60 columns. How do I avoid that?"
Why do you want to avoid that?